Metagenome-Assembled Genome: SRR13061492_bin.11_MetaWRAP_v1.3_MAG
This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR13061492 of study SRP292586.
INSDC center name
EMG
Submitter Id
SRR13061492_bin.11_MetaWRAP_v1.3_MAG
assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software
metaspades v3.15.3
binning parameters
MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.
binning software
MetaWRAP v1.3
broad-scale environmental context
human digestive system
broker name
EBI-EMG
collection date
2018-01
completeness score
63.74
completeness software
CheckM
contamination score
0.0
environmental medium
saliva
geographic location (country and/or sea)
Denmark
geographic location (latitude)
55.67
geographic location (longitude)
12.57
investigation type
metagenome-assembled genome
isolation_source
oral metagenome
local environmental context
oral cavity
metagenomic source
oral metagenome
project name
The purpose of the present investigation was to use the oral cavity as an in-vivo model to study the impact of internal and external perturbations on bacterial biofilm communities. We tested the hypotheses that bacterial gene expression of the healthy microbiota reflects habituation to site-specific ecological perturbations, and that the perturbation effect of chronic inflammation, periodontitis, impacts bacterial gene expression not only locally, but also at other sites of the oral cavity. Oral microbial samples were collected from three oral sites plaque, tongue and saliva from patients with periodontitis and healthy controls. Paired metagenomics and metatranscriptomics were used to perform concomitant characterisation of taxonomic composition and to determine species specific bacterial activity as expressed by the ratio of messenger RNA to the corresponding genomic DNA.
sample derived from
SAMN16796830
sample name
SRR13061492_bin.11_MetaWRAP_v1.3_MAG
scientific_name
uncultured Candidatus Saccharimonas sp.
sequencing method
Illumina HiSeq 2500
taxonomic classification
The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Candidatus Saccharibacteria;c__;o__;f__;g__Candidatus Saccharimonas;s__
taxonomic identity marker
multi-marker approach